[BioC] 'recursive default argument' error in GOENTREZID2GO

[Oleg Sklyar]

Does not it look like a bug in R, Should not it be reported as such, 
Diego could you maybe do that? I did hit many ^C before getting my error 
as I had large objects and often used ^C to terminate printing. And 
well, quitting R is *not* a solution, such things run in scripts and 
need to be stable.

Best,
Oleg

Diego Diez wrote:
> Hi Oleg, James and Seth.
> 
> I also found the same problem (or very close) and used the same approach 
> mentioned by James to solve it, which works fine but still it too 
> annoying. After reading the post I've tried to reproduce the steps that 
> use to reach me to that point. It happens with any environment, or at 
> least annotation packages stored as environments. I can't think of any 
> reason why this happens but let me show you the code:
> 
>  > library(rae230a)
>  > xx <- as.list(rae230aENTREZID)
> ^C
>  > xx <- as.list(rae230aENTREZID)
> Error in as.list(rae230aENTREZID) : recursive default argument reference
> 
> now, while the as.list() is working, cancel the process with control-C, 
> and after that, the mentioned error happens whenever you try to repeat 
> the process of transforming the environment to a list. The cancel must 
> be done soon after hitting return, I found one case when delaying a 
> little made me unable to reproduce the error. Other environments found 
> in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc).
> 
> Going deeper to the problem, I found that canceling the environment 
> "loading" with any function reproduces the problem:
> 
>  > is(rae230aSYMBOL)
> ^C
>  > is(rae230aSYMBOL)
> Error in .class1(object) : recursive default argument reference
>  > rae230aSYMBOL
> Error: recursive default argument reference
> 
> By "loading" a mean that the first time I execute as.list(rae230aSYMBOL) 
> or is(rae230aSYMBOL) there is a delay which I assume is the environment 
> being loaded into memory. Any further execution of the same commands 
> will occur almost immediately.
> 
> So, why should I cancel an environment loading soon after trying to load 
> it? It happens that I was loading an environment inside a function, ran 
> the function and wanted to cancel the execution, thus, the error 
> appeared and the environemnt was unusable. Anyway, this seems to me more 
> an R related issue.
> 
> HTH,
> 
> Diego.
> 
> 
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> powerpc-apple-darwin8.9.1
> 
> locale:
> C
> 
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
> [7] "base"
> 
> other attached packages:
>  rae230a
> "1.16.0"
>  >
> 
> 
> 
> On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote:
> 
>> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
>>
>>> Hi Oleg,
>>>
>>> Oleg Sklyar wrote:
>>>> Hi,
>>>>
>>>> anybody has an idea as for the following error, the example is actually
>>>> from the GO package examples. Thanks, Oleg
>>>>
>>>>> library(GO)
>>>>> egId <- "10043"
>>>>> egIdGoData <- GOENTREZID2GO[[egId]]
>>>> Error: recursive default argument reference
>>>
>>> I sometimes see that error as well. I have no idea what causes it, as it
>>> doesn't seem repeatable. Anyway, quitting R and starting over has always
>>> fixed the problem for me.
>>
>> Oleg, is this reproducible for you?  I wasn't able to get the error.
>> Have you tried updating to R patched?
>>
>> + seth
>>
>> --Seth Falcon | Computational Biology | Fred Hutchinson Cancer 
>> Research Center
>> http://bioconductor.org
>>
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-- 
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466